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X-ray/Neutron joint refinement
by Emily Golden 19 Jun '13

19 Jun '13

Hi All, I have a couple of questions about X-ray/neutron joint refinement in phenix. Is it possible to use the neutron data only for refining hydrogen atom positions and the X-ray data for all other atoms? I used the option to add hydrogen atoms to model and refine H/D at exchangable sites and H elsewhere. This worked for many of the exchangeable hydrogen atoms. However, for some side chains, especially Lysine, the program has placed a hydrogen and deuterium atom (with refined occupancies) in the same position as the atom it is supposed to be bonded to. Does anybody know why this is happening and what I may be able to do about it. Or will I need to manually move each misplaced H/D in Coot? Thank you for your help. Emily

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Jerry Karle
by Robert Sweet 19 Jun '13

19 Jun '13

Jerry Karle died a couple of weeks ago, and one of us here learned about it by noticing his obituary in the NY Times: http://www.nytimes.com/2013/06/15/health/jerome-karle-94-dies-nobelist-for-… He's well known to those of us who started in this field when the solving of a Patterson function for a heavy atom in a structure was the only way we knew to get the structure. With Herb Hauptman, and in close teamwork with his wife Isabella who actually >did< crystallography, he played a major role in working out the sort of Direct Methods that allowed one to solve ordinary small-molecule structures before the days of high-speed computing. As the obituary points out, Jerry and Herb shared the 1985 Nobel Prize in Chemistry for this work. The obit. is worth reading. I suspect you'll see an even better one in Nature soon. My own tiny personal memory of Jerry Karle: When I was a grad student at the Univ. of Wisc. with Larry Dahl I made a pilgrimage to the NRL to visit Jerry and Isabella. I was trying to use direct methods to solve at least one cephalosporin structure, which eventually appeared in my thesis, and there was a feature of DM that I failed to understand. They were very patient with me, but couldn't understand what it was I didn't get. It turns out to have been essentially trivial, but that's the way it goes sometimes. Anyway he always recognized me afterwards, or pretended to. I was delighted on arriving at BNL to discover that his daughter Louise was here. Bob ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Re: [phenixbb] cv convert to mtz file
by Pavel Afonine 17 Jun '13

17 Jun '13

Hi Majid, I had no problems converting cbh1_c10a.cv into MTZ using Phenix "Reflection file editor". To convert he other one (cbh1_fg34.cv) you need to add CRYST1 record similarly to cbh1_c10a.cv. Make sure you use recent version of Phenix.. Pavel On 6/17/13 5:48 AM, Majid Haddad Momeni wrote: > Dear Sir/Madam, > > I need help to be able to convert my .cv file to mtz, I have already tried both ccp4 package and Phenix through "Convert to/modify/extend MTZ" and "Reflection file editor" > However they didn't work! > I do highly appreciated of your assistance, > > Best Regards > Majid Haddad Momeni > PhD Student > Swedish University of Agricultural Sciences, > Uppsala-Sweden

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Beamtime available at NE-CAT (APS)
by Cyndi Salbego 14 Jun '13

14 Jun '13

Synchrotron beam time available to general users at NE-CAT (Sector 24 of APS) during the month of July 24ID-C beamline features: - Undulator beamline fully tunable from 6 to 21 keV (2.1 to 0.6 Angstroms) - PILATUS 6M pixel array detector, allowing continuous fine phi-sliced data acquisition at up to 25 frames per second - MD2 microdiffractometer with triple aperture (70, 30, or 10 micron apertures) - MK3 mini-kappa available on the microdiffractometer allowing reorientation of crystals for better diffraction geometry. - ALS style sample mounting robot compatible with ALS pucks or Unipucks 24ID-E beamline features: - Fixed energy undulator beamline (12662 eV) optimized for Se-SAD data collection - Beam stability optimized for smaller beams (down to 5 micron) - ADSC Q315 CCD detector - MD2 microdiffractometer with triple aperture (50, 20, or 5 micron apertures) - ALS style sample mounting robot compatible with ALS pucks or Unipucks - Remote data collection available For more info on our beamlines and updated schedule availability please see necat.chem.cornell.edu or contact Cyndi Salbego (csalbego(a)anl.gov). To apply for General User Time (Rapid Access for 2013-2 run) please go to: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NE-CAT 630.252.0689

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Re: [phenixbb] elbow
by Mengbin Chen 13 Jun '13

13 Jun '13

Dear Dr. Dias, I tried the command line in Terminal, but Elbow still regularized the conformation and bonds of the ligand and the result turned out to be the same with that I ran thorough GUI. The thing is that the input pdb file has a conformation the ligand should adopt so that I do not really want energy minimization or geometry optimization to be done on it. Although I set "none" for "geometry optimization" in GUI, it unfortunately changed the ligand conformation. Thank you, Mengbin On Thu, Jun 13, 2013 at 2:52 PM, Mengbin Chen <mengbinc(a)sas.upenn.edu>wrote: > Dear Dr. Dias, > > I tried the command line in Terminal, but Elbow still regularized the > conformation and bonds of the ligand and the result turned out to be the > same with that I ran thorough GUI. The thing is that the input pdb file has > a conformation the ligand should adopt so that I do not really want energy > minimization or geometry optimization to be done on it. Although I set > "none" for "geometry optimization" in GUI, it unfortunately changed the > ligand conformation. > > Thank you, > Mengbin > > > On Thu, Jun 13, 2013 at 2:42 PM, Joao Dias <joao.dias(a)heptares.com> wrote: > >> Dear Mengbin, >> You can open a terminal window and run elbow as a command line. >> >> phenix.elbow --final_geometry input_file.pdb**** >> >> >> Do not forget to initialize the phenix environment, depending on your >> terminal shell, one example is: >> source >> /Applications/PHENIX-dev-1320/Contents/phenix-dev-1320/phenix_env.sh >> >> All the best, >> Joao >> >> Dr Joao Dias**** >> >> Principal Scientist**** >> >> ** ** >> >> Heptares Therapeutics Ltd**** >> >> BioPark, Broadwater Road,**** >> >> Welwyn Garden City,**** >> >> Herts, AL7 3AX**** >> >> UK >> >> From: Mengbin Chen <mengbinc(a)sas.upenn.edu> >> Reply-To: PHENIX user mailing list <phenixbb(a)phenix-online.org> >> Date: Thursday, 13 June 2013 19:32 >> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> >> Subject: [phenixbb] elbow >> >> Dear PHENIX Users, >> >> I have been playing around with Elbow for a while, but I kept having >> problems generating .cif file. For "Chemical file type" and "Template PDB >> file", I used the pdb file of the ligand. Since the coordinates in the pdb >> file corresponds to a conformation desired, I chose "None" for "geometry >> optimization". After running Elbow, the output pdb file was completely >> different than the input one -- even double bonds became single bonds and >> 10-membered ring conformation changed. I have tried Sketcher in CCP4 >> package, but no good results either. Could anyone tell me how to do this >> correctly? Any help is appreciated! >> >> Thank you in advance, >> Mengbin >> >> -- >> Mengbin Chen >> Department of Chemistry >> University of Pennsylvania >> >> [image: www.heptares.com] <http://www.heptares.com><http://www.heptares.com> >> >> >> The information in this e-mail is confidential and may be legally >> privileged. It is intended for the exclusive attention of the addressee >> stated above and should not be copied or disclosed to any other. If you >> have received this transmission in error, please make no use of its >> contents and contact the sender. Contact and registered office address: >> Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden >> City, Hertfordshire, AL7 3AX. Company No: 06267989 >> >> > > > -- > Mengbin Chen > Department of Chemistry > University of Pennsylvania > -- Mengbin Chen Department of Chemistry University of Pennsylvania

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elbow
by Mengbin Chen 13 Jun '13

13 Jun '13

Dear PHENIX Users, I have been playing around with Elbow for a while, but I kept having problems generating .cif file. For "Chemical file type" and "Template PDB file", I used the pdb file of the ligand. Since the coordinates in the pdb file corresponds to a conformation desired, I chose "None" for "geometry optimization". After running Elbow, the output pdb file was completely different than the input one -- even double bonds became single bonds and 10-membered ring conformation changed. I have tried Sketcher in CCP4 package, but no good results either. Could anyone tell me how to do this correctly? Any help is appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"
by Sam Stampfer 12 Jun '13

12 Jun '13

Dear Phenix Community, I am preparing my structure for deposition and ran it through the Generate "Table 1" function in phenix. The inputs I gave it were my .mtz structure factors file, the final pdb coordinate file, and the log file from hkl2000. I did not provide unmerged data. My pdb file (which had been refined using phenix.refine) had values of r_work=0.2342 r_free=0.2603 However, phenix.model_vs_data (from Generate "Table 1") gave me r_work=0.2940 r_free=0.3150 I also got this warning about resolution limits, but I think it should not have affected the R-free calculation to this extent: WARNING: Resolution limits in scaling log for structure A549T are inconsistent with resolution limits in the MTZ file: 50.00 - 3.02 (in logfile) 48.47 - 3.03 (in MTZ file) When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in the documentation that twinning can account for some of this discrepancy, but that the program is supposed to take twinning into account if it will lower the calculated R-work by more than 2%, which it doesn't seem to have done (or there is some other problem with my data). Thanks for your help! -Sam

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den refinement
by Andreas Förster 12 Jun '13

12 Jun '13

Dear all, I'm trying to get DEN refinement going from the command line. The run aborts quickly with the following error in the log file: Sorry: Cartesian simulated annealing should not be turned on for DEN refinement. Annealing settings are controlled in the den parameter scope. The DEN scope in input.def looks like this: den { reference_file = den_ref_Jun.pdb gamma = 0.5 kappa = 0.1 weight = 30 sigma = 0.44 optimize = True opt_gamma_values = 0 0.2 0.4 0.6 0.8 1 opt_weight_values = 3 10 30 100 300 num_cycles = 12 kappa_burn_in_cycles = 2 bulk_solvent_and_scale = True refine_adp = True final_refinement_cycle = False verbose = False annealing_type = *torsion cartesian output_kinemage = False restraint_network { lower_distance_cutoff = 3 upper_distance_cutoff = 15 sequence_separation_low = 0 sequence_separation_limit = 10 exclude_hydrogens = True ndistance_ratio = 1 export_den_pairs = False den_network_file = None } Annealing type is torsion from what I can tell. What am I doing wrong? (Release tag: 1394, Platform: intel-linux-2.6-x86_64 redhat-e6.2) Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Discrepancy between phenix.refine and phenix.model_vs_data R-factors
by Abhinav Kumar 11 Jun '13

11 Jun '13

I am getting a significant difference between the R-factors written by phenix.refine and phenix.model_vs_data. 1. Phenix.refine phenix.refine "in.pdb" "Fobs.mtz" "refinement.input.xray_data.labels=FP SIGFP" "refinement.input.xray_data.high_resolution=2.50" "fix_rotamers=True" "ordered_solvent=True" "strategy=tls+individual_sites+individual_adp" Final R-work = 0.1829, R-free = 0.2141 2. Phenix.model_vs_data phenix.model_vs_data out.pdb Fobs.mtz f_obs_label="FP" r_free_flags_label="FreeR_flag" high_resolution=2.50 comprehensive=true r_work(re-computed) : 0.1808 r_free(re-computed) : 0.2099 How can I reproduce the phenix.refine R-factors in phenix.model_vs_data? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992

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phenix elbow: is similar compound helpful to create restraint for new ligand?
by Rongjin 11 Jun '13

11 Jun '13

Hello Phenix users, I have tetrabutylphosphonium in my crystal. I found a similar compound tetrabutylammonium (PDB residue name TBA) which are found in several PDB entries. Usually I draw the new compound in 2-D format and convert to 3D and then create restrain files. In this case, considering N and P are very similar, will the TBS be helpful for elbow to generate restrains for tetrabutylphosphonium? Thanks Rongjin Guan

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Hi
by Wei Shi 10 Jun '13

10 Jun '13

Hi all, I was trying to solve the structure of a protein in several different datasets using xds and phenix. I could solve the structure from one dataset in space group P4. For another dataset, I could solve the structure using the monomer of the structure I got from the first dataset as search model and solve the structure in space group mC. For the third dataset, in IDXREF.LP, the space group of the highest symmetry is hp: 101.2, 101.3, 58.8, 90, 90, 120. According to Mathiews coefficient, 1 monomer is expected in the asymmetric unit. But I couldn't get the molecular replacement solution using the same method as for the second dataset. I also tried several other search models (eg. deletion of the potential flexible region in the search model) and tried to find the solution in all possible pointgroup. I also tried to process the data in oC (C222), the space group of the second highest symmetry in IDXREF.LP, but, still I could not get right molecular replacement solution. I don't whether this means that there is a big conformational change for the structure in the third dataset or the space group I use is not right. Let me know if any of you would have any comments or suggestions for me. Thank you so much! Best, Wei

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Postdoc Position - Berkeley
by Paul Adams 07 Jun '13

07 Jun '13

Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 76029 Division: Physical Biosciences (Joint BioEnergy Institute) Date Opened: 6/5/2013 Summary: A postdoctoral position is available at the Joint BioEnergy Institute in Emeryville to work on proteins involved in plant cell wall synthesis. To learn more about JBEI visit: http://www.jbei.org/ Duties: Implementation of methods for the cloning, protein expression, and purification for glycosyl transferases, typically using the Gateway system for gene manipulation. Transformation of host organisms for protein expression, followed by assay of protein expression, and scale up of expression and sample processing (such as deglycosylation). Purification of proteins for biochemical and structural studies. Expression in multiple systems, including E. coli, yeast and insect cells. Qualifications: a Ph.D. in biochemistry, molecular biology, structural biology, or a related field. Demonstrated experience with protein expression, especially in systems other than E. coli. First-author publications demonstrating prior results in the area of protein expression. Experience with cloning methods and protein purification methods. Strong problem solving skills. Solid interpersonal skills and the ability to work in a team environment are critical. Experience with the practical aspects of structure solution by X-ray crystallography would be helpful but not essential. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years, and 57 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 76029 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=76029 -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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From Dmitri Svergun and Matthias Wilmanns: BSR-2013: Abstract submission deadline is extended until 20th June!
by Terwilliger, Thomas C 07 Jun '13

07 Jun '13

11th International Conference: Biology and Synchrotron Radiation (BSR), 8-11 September 2013, EMBL Hamburg, Germany The abstract submission deadline for BSR-2013 is extended until Thursday 20th June, 2013! Biologists, physicists, chemists, from students to principal investigators, are invited to this tri-annual meeting with rich traditions. Do not miss the unique opportunity to present your work, meet colleagues, friends and future collaboration partners from all over the world. Check out our preliminary programme to learn more. BSR 2013 offers a tour of DESY’s most impressive research infrastructures and includes a broad social programme to discover the vibrant city of Hamburg. Accompanying persons will enjoy special rates! Extended deadlines: ·Registration and abstract submission: 20 June 2013 ·Registration without abstract: 15 August 2013 Take a look at the updates BSR webpage ( www.bsr2013.org<http://www.bsr2013.org/>) for more information and to register. CONTACT: Diah.Yulianti(a)embl.de<mailto:[email protected]>, or margret.fischer(a)embl-hamburg.de<mailto:[email protected]> Alternatively, contact us on the event facebook page

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Re: [phenixbb] Pseudotranslation issue
by Gino Cingolani 07 Jun '13

07 Jun '13

Dear Fulvio, We just had a similar problem (further complicated by some twinning). Assuming that: 1. You collected enough data and 2. You don't have a crazy number of molecules in the tetragonal asymmetric unit, I would advice to scale your data in P1 and do MR in P1. Then use conventional refinement + model building to bootstrap a better model (most likely your initial model isn't as good). Rosetta may help, too. Then eventually go back to the tetragonal data with the improved search model and see if LLG and packing make sense. Gino **************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org **************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) Fulvio Saccoccia <fulvio.saccoccia(a)uniroma1.it> wrote: >Dear phenixbb, > I have a data set collected at 2.2A resolution that I can integrate >in P4. Aimless, Phaser and Xtriage recognized a pseudotranslation >(34.6% of origin peak) at fractional coordinates 0.500 0.500 0.479 >(ORTH 46.7 46.7 37.4). However labelit.index run with >sublattice_allow=true search did not detect the pseudotranslation >vector. So far, any attempts to phase by molecular replacement was >unsuccesfull and I suspect that it could be due to incorrect assignement >of space group: > >Now, some questions arise: >1) does the pseudo translation exist or do not? >2) if translational NCS is present, could it mimic a P41/P42/P43 space >group? >3) in any case, any advices in order to properly deal with tNCS will be >of great help? > >I thank you in advance >Best wishes > >-- >Fulvio Saccoccia, PhD >Sapienza University of Rome >Dept. of Biochemical Sciences "A. Rossi Fanelli" >Piazzale Aldo Moro, 5 >00185 Rome (Italy) > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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Pseudotranslation issue
by Fulvio Saccoccia 07 Jun '13

07 Jun '13

Dear phenixbb, I have a data set collected at 2.2A resolution that I can integrate in P4. Aimless, Phaser and Xtriage recognized a pseudotranslation (34.6% of origin peak) at fractional coordinates 0.500 0.500 0.479 (ORTH 46.7 46.7 37.4). However labelit.index run with sublattice_allow=true search did not detect the pseudotranslation vector. So far, any attempts to phase by molecular replacement was unsuccesfull and I suspect that it could be due to incorrect assignement of space group: Now, some questions arise: 1) does the pseudo translation exist or do not? 2) if translational NCS is present, could it mimic a P41/P42/P43 space group? 3) in any case, any advices in order to properly deal with tNCS will be of great help? I thank you in advance Best wishes -- Fulvio Saccoccia, PhD Sapienza University of Rome Dept. of Biochemical Sciences "A. Rossi Fanelli" Piazzale Aldo Moro, 5 00185 Rome (Italy)

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rosetta installation problems
by Mengbin Chen 04 Jun '13

04 Jun '13

Dear Phenix Users, I am interested in using Rosetta to do MR, but unfortunately I have encountered some problems in installing it: I was able to get to the step where "scons: done building targets." showed up, and set up the environment by typing setenv /Users/yanghai/Desktop/rosetta-3.5 into the shell. I also filled out the "path to rosetta" in "Preferences" under "PHENIX GUI", which I believe it is correct. However, when I was ready to run MR-rosetta, it kept saying "cannot locate Rosetta programs. You may set the path in PHENIX GUI under preferences->Automation, or define the environment variable PHENIX_ROSETTA_PATH (recommended)". Any help would be apprecited! Thank you in advance, Mengbin Chen -- Mengbin Chen Department of Chemistry University of Pennsylvania

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EG4 not in phenix dictionary?
by Yarrow Madrona 03 Jun '13

03 Jun '13

Hello, I have previously refined EG4 and EG2 (tetra and diethylene glycol) as ligands and these were in the standard phenix library. I was under the impression that phenix shares the library from the CCP4 monomer library which I know should have EG4. Can anyone help me with this. I guess the alternative is to generate a restraints file. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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MAX IV Life Science Director position
by Derek Logan 03 Jun '13

03 Jun '13

Hi, If anyone fancies becoming Life Science Director at the world's brightest light source, look no further than here: http://www.lunduniversity.lu.se/o.o.i.s?id=24914&Dnr=547454&Type=E /Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/node/307<http://www.maxlab.lu.se/node/307> Lund University, Box 124, 221 00 Lund, Sweden

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Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"
by Michael Thompson 01 Jun '13

01 Jun '13

As another follow up to this point, I have had a recent example where Xtriage reported that my intensity statistics indicated twinning (<|L|>=0.399 and <L^2>=0.227, alpha=0.4). After having refined the structure with the suggested twin law, and making composite omit maps along the way (using autobuild with no twin law), I ran model vs. data at the end of refinement and noticed that it reported R/Rfree that were about 10% higher than the R/Rfree from refinement, similar to what the original post described. I checked the model vs. data logfile and found that the L-test routine used by model vs. data was failing, so the subsequent analysis was carried out as if there was no twinning. So in my case, the crystal was twinned, but model vs. data was not able to perform the L-test so it was outputting incorrect R-factors. The error message at the top of the model vs. data log file is: Twin analysis failed: Python argument types in l_test.__init__(l_test, miller_index, double, space_group, bool, float, float, float, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor> miller_indices, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> intensity, cctbx::sgtbx::space_group space_group, bool anomalous_flag, long parity_h, long parity_k, long parity_l, unsigned long max_delta_h) Twin analysis failed: Python argument types in l_test.__init__(l_test, miller_index, double, space_group, bool, float, float, float, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor> miller_indices, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> intensity, cctbx::sgtbx::space_group space_group, bool anomalous_flag, long parity_h, long parity_k, long parity_l, unsigned long max_delta_h) Perhaps there are some other users who are seeing this behavior because the L-test fails within model vs. data. Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Wednesday, May 29, 2013 5:18:57 PM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1" On Wed, May 29, 2013 at 4:13 PM, Sam Stampfer <Samuel.Stampfer(a)tufts.edu> wrote: > When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in > the documentation that twinning can account for some of this discrepancy, > but that the program is supposed to take twinning into account if it will > lower the calculated R-work by more than 2%, which it doesn't seem to have > done (or there is some other problem with my data). Okay, the problem is that your data don't actually appear to be twinned. The automatic method used by phenix.model_vs_data (which is used internally for Table 1 and the validation GUI) only tries possible twin laws if the results of the "L test" show a suspicious distribution of intensities. Your data look fine, so it doesn't bother trying the twin laws. That the R-factors are lower when you refine with a twin law isn't necessarily indicative of the data actually being twinned - Garib Murshudov has looked into this in detail but I confess to being ignorant of the math (but I can probably dig up his paper on the subject if anyone is interested). However, I'm pretty sure the data are actually in a higher-symmetry space group. Will send details and new files off-list (probably tomorrow at this rate). I should probably change some of the programs and/or documentation to make it more clear what is being done internally, since it took me a bit of digging to realize what was going on. In general, though, always be very careful before running twinned refinement! I have seen several users do this by mistake when they really had higher symmetry. The maps will also be more model-biased when using twinned refinement, so it's good to avoid doing this unless absolutely necessary. -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Re: [phenixbb] refinement of partly occupied water molecules?
by krimmer＠staff.uni-marburg.de 31 May '13

31 May '13

Dear Nathaniel, dear Pavel, thank you for your fast answers! > currently phenix.refine can add automatically only fully occupied > waters (I am not sure it will ever use atomic model for partially > occupied waters). If necessary, add partially occupied waters > yourself manually. Make sure they have properly set altlocs > (alternative location identifiers): non blank (say A and B). Is it current praxis to let phenix.refine freely refine the occupancy of water molecules (adding partially occupied water molecules in coot and don’t fix the occupancy in phenix)? If I do so, these water molecules are refined by phenix.refine with occupancies between 0.4-0.8. My resolution range was 1.1 – 1.4 Å. > The nightly builds have an option in phenix.refine to place ions > automatically based on a variety of criteria (still being tuned). > However, what you describe doesn't sound like any ion coordination > motif that I've read about. Could you please send us a picture that > shows the density in context? Some of the other readers with more > experience in "blobology" may recognize it. [if our list server > complains about the size of the message, just ignore it, I'll approve > it for posting] Attached you will find the image of the blob. I think it’s easily visible that the density blob is in the middle of the five-ring and that there is also a (smaller) blob in the middle of the six-ring. The water which occupies the blob was not yet refined with phenix, I just put it there to measure the distances to the carbon atoms. Best regards, Stefan

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gap between Wilson B and average B
by fn1＠rice.edu 30 May '13

30 May '13

Dear all, I have a structure at about 3.5 A, which has a wilson B of about 109 and has an average B factor from model is only 49 (I did not use TLS). I read from the previous posts that wilson B is sometimes smaller than average B, but in my case it is reversed. I look at the distribution of model B factors, they are in the range of 8 to 132. Is there any problem with the refinement of this structure? Thanks in advance for all advice! Regards, Fengyun

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refinement of partly occupied water molecules?
by krimmer＠staff.uni-marburg.de 30 May '13

30 May '13

Dear all, I have a question concerning the refinement of partly occupied water molecules: in some of my macromolecular crystal structures with resolutions between 1.1 - 1.4 Å, mainly in the second solvation shell round positive Fo-Fc electron density blobs are detectable which show after assignment of a water molecule to these blob and subsequent refinement with Phenix refine a good-looking calculated 2Fo-Fc electron density (round shape, the 2Fo-Fc map appears at a contour level of σ = 1.0 - 1.4), but there also occurs a small negative Fo-Fc electron density detectable inside the 2Fo-Fc density blob. The negative Fo-Fc electron density disappears if the occupancy of the water molecule is refined by Phenix or manually set lower than 100% occupancy. Therefore, I think these positions are partly occupied by water molecules, but I am not sure how I should handle it/how it is generally handled. I would be thankful for any advice and/or literature about this topic. My second question is concerning a density blob in perfect coordination distance to an indolyl group (perfectly located in the middle of the five-ring, with 3.4 Å distance to every of the five carbon atoms of the five-ring). What‘s the best way to find out which ion possibly occupies this position? I tried Na+ and Ca2+, but after refinement big negative Fo-Fc blobs appear in both cases (maybe the ion at this position is only partly occupied?). There is no anomalous signal detectable at this position (data collection wavelength was 0.91841 nm). After the refinement of a water molecule at this position, a positive Fo-Fc election density is still there. Thank you for your help! Stefan

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R-merge
by Mengbin Chen 29 May '13

29 May '13

Dear Phenix Users, I have R-merge values equal 0.000 from highest resolution shell (which corresponds to values larger than 1.000) in a data set processed by HKL2000, with redundancies higher than 10 (I know this may help in increasing R-merge). I am not sure if this is going to be a problem of Table 1 for the reviewers. Could you kindly drop me your suggestions? Thank you in advance, Mengbin Chen -- Mengbin Chen Department of Chemistry University of Pennsylvania

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phenix.refine using anomalous concepts for neutron data?
by Derek Logan 29 May '13

29 May '13

Hi, I'm doing a joint X-ray neutron refinement in Phenix and have run into some behaviour that puzzles me. I had not been paying any attention to the use or non-use of anomalous signal in the neutron dataset, as This is what I get if I let phenix.refine itself decide whether or not to use anomalous data: ================================= Neutron data ================================ F-obs: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Observation type: xray.reconstructed_amplitude Type of data: double, size=16672 Type of sigmas: double, size=16672 Number of Miller indices: 16672 Anomalous flag: True Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.785008 Completeness with d_max=infinity: 0.78486 Bijvoet pairs: 6832 Lone Bijvoet mates: 1750 Anomalous signal: 0.0876 Number of F-obs in resolution range: 16672 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 29.2200 d_min = 1.8983 and this is what I get if I forcibly switch off use of anomalous data in the phenix.refine GUI: ================================= Neutron data ================================ F-obs: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Observation type: xray.reconstructed_amplitude Type of data: double, size=16672 Type of sigmas: double, size=16672 Number of Miller indices: 16672 Anomalous flag: True Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.785008 Completeness with d_max=infinity: 0.78486 Bijvoet pairs: 6832 Lone Bijvoet mates: 1750 Anomalous signal: 0.0876 force_anomalous_flag_to_be_equal_to=False Reducing data to non-anomalous array. R-linear = sum(abs(data - mean(data))) / sum(abs(data)) R-square = sum((data - mean(data))**2) / sum(data**2) In these sums single measurements are excluded. Redundancy Mean Mean Min Max Mean R-linear R-square unused: - 29.2234 bin 1: 29.2234 - 4.0863 1 2 1.699 0.0240 0.0011 bin 2: 4.0863 - 3.2448 1 2 1.793 0.0302 0.0022 bin 3: 3.2448 - 2.8350 1 2 1.800 0.0417 0.0041 bin 4: 2.8350 - 2.5760 1 2 1.764 0.0486 0.0054 bin 5: 2.5760 - 2.3914 1 2 1.745 0.0505 0.0051 bin 6: 2.3914 - 2.2505 1 2 1.717 0.0513 0.0051 bin 7: 2.2505 - 2.1378 1 2 1.658 0.0533 0.0056 bin 8: 2.1378 - 2.0448 1 2 1.614 0.0611 0.0074 bin 9: 2.0448 - 1.9661 1 2 1.575 0.0634 0.0075 bin 10: 1.9661 - 1.8983 1 2 1.485 0.0736 0.0097 unused: 1.8983 - Fobs statistics after all cutoffs applied: Miller array info: None Observation type: xray.amplitude Type of data: double, size=9840 Type of sigmas: double, size=9840 Number of Miller indices: 9840 Anomalous flag: False Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.855801 Completeness with d_max=infinity: 0.855503 What's going on here? If I let phenix.refine decide automatically, it looks like it's reading in F+ and F- separately and regarding them as independent in the refinement. If I force "no anomalous" it merges them. However I can't work out whether in either case it has actually read FOBS instead of the Friedel mates. According to the SCALA manual the I+ and I- columns will always be written out even if the keyword ANOMALOUS OFF is used, so this is a potential pitfall for many. In addition, phenix.refine seems to identify the neutron data first as xray.reconstructed_amplitude then as xray.amplitude even though the data are explicitly defined as neutron data in the GUI. I can send more information if required! Thanks Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/node/307<http://www.maxlab.lu.se/node/307> Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com<http://www.saromics.com>

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Structure Comparison questions
by Heather Condurso 29 May '13

29 May '13

Dear all, I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies? I will try a few things but any advice would be greatly appreciated. Heather condurso(a)bc.edu

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